Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
nf-core/sammyseq is a bioinformatics pipeline for the analysis of Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, a cheap and effective methodology to analyze chromatin state as described in:
Sebestyén, E., Marullo, F., Lucini, F. et al. SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome. Nat Commun 11, 6274 (2020). https://doi.org/10.1038/s41467-020-20048-9. Pubmed
Please note that this pipeline is under active development and has not been released yet.
Here is an outline of the analysis steps:
- Read QC (
- Trim reads to remove adapter sequences and low quality ends (
- Align on a reference genome (
- Remove duplicate reads (
- Generate alignment statistics (
- Create single track profiles in bigwig format (
- (Optionally) Generate pairwise comparison tracks in bigwig format if provided a list of the desired sample pairs ([
- Generate an analysis report by collecting all generated QC and statistics (
First, prepare a samplesheet with your input data that looks as follows:
Each row represents a fastq file (single-end) or a pair of fastq files (paired end),
experimentalID represents the biological specimen of interest and
sample the library produced for each fraction, it usually is a unique combination of
Now, you can run the pipeline using:
Please provide pipeline parameters via the CLI or Nextflow
-params-file option. Custom config files including those
provided by the
-c Nextflow option can be used to provide any configuration except for parameters;
For more details about the output files and reports, please refer to the output documentation.
nf-core/sammyseq was written by Lucio Di Filippo and Margherita Mutarelli and was based on the original pipeline developed in-house by SAMMY-seq creators.
We thank the following people for their extensive assistance in the development of this pipeline:
The development of this pipeline was made possible thanks to the projects Progetti@CNR Myo-CoV-2 B93C20046330005, AFM Téléthon EDMD-GenomeSCAN B53C22009260007 and PIR01_00011 I.Bi.S.Co. Infrastruttura per Big data e Scientific COmputing (PON 2014-2020).
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
An extensive list of references for the tools used by the pipeline can be found in the
You can cite the
nf-core publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.